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MetaCyc Enzyme: glycine oxidase

Gene: thiO Accession Number: BSU11670 (MetaCyc)

Synonyms: yjbR, goxB, FAD-dependent glycine oxidase

Species: Bacillus subtilis subtilis 168

Subunit composition of glycine oxidase = [ThiO]4
         glycine oxidase monomer = ThiO

Summary:
The thiO gene of Bacillus subtilis encodes an FAD-dependent glycine oxidase. This enzyme is a homotetramer with a monomer molecular mass of 42 kDa [Nishiya98, Settembre03]. ThiO is related to sarcosine oxidase and D-amino acid oxidase and uses an FAD cofactor and possibly a hydride transfer mechanism. The monomer contains two domains - a FAD-binding domain and a substrate binding domain [Settembre03].

The gene was cloned and overexpressed in Escherichia coli, and the recombinant protein was purified to homogeneity and characterized. The recombinant enzyme was shown to be a novel deaminating oxidase that catalyzed the oxidation of sarcosine, N-ethylglycine and glycine, as well as D-alanine, D-valine, and D-proline with lower activity. It produced the corresponding alpha-keto acids, ammonia/amine, and hydrogen peroxide [Nishiya98]. The enzyme can also oxidize the herbicide glyphosate [Pedotti09].

Oxidation of glycine catalyzed by ThiO generates the glycine imine intermediate 2-iminoacetate, an intermediate in thiamin diphosphate biosynthesis. A ThiO- mutant has an absolute requirement for the thiazole moiety of thiamin [Settembre03].

The structure of ThiO with N-acetylglycine bound at the active site was reported [Settembre03].

Locations: cytosol

Map Position: [1,243,735 -> 1,244,844]

Molecular Weight of Polypeptide: 40.937 kD (from nucleotide sequence), 42.0 kD (experimental) [Settembre03 ]

Unification Links: DBTBS Operons:goxB , Entrez:2633521 , GenoList (SubtiList):BSU11670 , GOA:O31616 , Protein Model Portal:O31616 , SMR:O31616 , String:224308.BSU11670 , String:BSU11670 , SubtilisWiki:thiO , SubtiWiki:thiO , UniProt:O31616

Relationship Links: InterPro:IN-FAMILY:IPR006076 , InterPro:IN-FAMILY:IPR012727 , PDB:Structure:1NG3 , PDB:Structure:1NG4 , PDB:Structure:1RYI , PDB:Structure:3IF9 , Pfam:IN-FAMILY:PF01266

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0009228 - thiamine biosynthetic process Inferred by computational analysis [GOA00]
GO:0009635 - response to herbicide Inferred by computational analysis [GOA00]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [GOA00]
Molecular Function: GO:0016491 - oxidoreductase activity Inferred by computational analysis [GOA00, GOA01a]
GO:0043799 - glycine oxidase activity Inferred by computational analysis [GOA01]
GO:0050660 - flavin adenine dinucleotide binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [GOA07, GOA00]

Gene Class: UNCLASSIFIED

Credits:
Imported from BsubCyc 15-Sep-2011 by Caspi R , SRI International
Revised 15-Sep-2011 by Caspi R , SRI International


Enzymatic reaction of: glycine oxidase/deaminase

EC Number: 1.4.3.19

glycine + oxygen + H2O <=> ammonium + hydrogen peroxide + glyoxylate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for glycine: cyclopropylglycine [Settembre03 ]

In Pathways: superpathway of thiamin diphosphate biosynthesis II , thiazole biosynthesis II (Bacillus) , butanol and isobutanol biosynthesis (engineered)

Cofactors or Prosthetic Groups: FAD [Settembre03]


Enzymatic reaction of: 2-iminoacetate deaminase (glycine oxidase)

2-iminoacetate + H+ + H2O <=> glyoxylate + ammonium

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is favored in the direction shown.

Cofactors or Prosthetic Groups: FAD [Settembre03]


Enzymatic reaction of: D-alanine oxidase (glycine oxidase)

EC Number: 1.4.3.19

D-alanine + H2O + oxygen <=> pyruvate + ammonium + hydrogen peroxide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.


Enzymatic reaction of: N-ethylglycine oxidase

EC Number: 1.4.3.19

N-ethylglycine + H2O + oxygen <=> glyoxylate + ethylamine + hydrogen peroxide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.


Enzymatic reaction of: sarcosine oxidase (glycine oxidase)

EC Number: 1.4.3.19

sarcosine + H2O + oxygen <=> glyoxylate + methylamine + hydrogen peroxide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.


Enzymatic reaction of: glycine oxidase

glycine + oxygen <=> 2-iminoacetate + hydrogen peroxide + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

Alternative Substrates for glycine: cyclopropylglycine [Settembre03 ]

In Pathways: superpathway of thiamin diphosphate biosynthesis II , thiazole biosynthesis II (Bacillus)

Cofactors or Prosthetic Groups: FAD [Settembre03]

Kinetic Parameters:

Substrate
Km (μM)
Citations
glycine
1120.0
[Settembre03]


References

GOA00: GOA (2000). "Gene Ontology annotation based on Swiss-Prot keyword mapping."

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA07: GOA, UniProt (2007). "Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping."

Nishiya98: Nishiya Y, Imanaka T (1998). "Purification and characterization of a novel glycine oxidase from Bacillus subtilis." FEBS Lett 438(3);263-6. PMID: 9827558

Pedotti09: Pedotti M, Rosini E, Molla G, Moschetti T, Savino C, Vallone B, Pollegioni L (2009). "Glyphosate resistance by engineering the flavoenzyme glycine oxidase." J Biol Chem 284(52);36415-23. PMID: 19864430

Settembre03: Settembre EC, Dorrestein PC, Park JH, Augustine AM, Begley TP, Ealick SE (2003). "Structural and mechanistic studies on ThiO, a glycine oxidase essential for thiamin biosynthesis in Bacillus subtilis." Biochemistry 42(10);2971-81. PMID: 12627963


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 19.0 on Thu Apr 2, 2015, BIOCYC13B.